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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ), 'gf_id' => 'HOM05D001536', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001536' ), 'data_identifier' => 'HOM05D001536', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001536', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '414', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A07p13020' => 'bna', 'A07p35660' => 'bna', 'A08p27430' => 'bna', 'A08p32160' => 'bna', 'A09p40010' => 'bna', 'A09p62600' => 'bna', 'Aa31LG1G1090' => 'aar', 'Aa31LG4G11510' => 'aar', 'Aa31LG7G8470' => 'aar', 'Actinidia01963' => 'ach', 'Actinidia01970' => 'ach', 'Actinidia04855' => 'ach', 'Actinidia12316' => 'ach', 'Actinidia19923' => 'ach', 'Actinidia31950' => 'ach', 'Actinidia33240' => 'ach', 'Ah.02g126590' => 'amhyb', 'Ah.11g048120' => 'amhyb', 'AL1G25780' => 'aly', 'AL1G39110' => 'aly', 'AL2G28470' => 'aly', 'Aqoxy3G00455' => 'aox', 'Aqoxy3G03549' => 'aox', 'arahy.Tifrunner.gnm1.ann1.B15RMV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BZ8U3A' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I4K7T0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PQMP7V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PU8JJL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SK753M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULDL2L' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W8C8ZP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZTLC2M' => 'arhy', 'AT1G13940' => 'ath', 'AT1G26620' => 'ath', 'AT1G69360' => 'ath', 'ATR0111G010' => 'atr', 'Atru.chr11.1694' => 'acertr', 'Atru.chr9.313' => 'acertr', 'AUR62003138' => 'cqu', 'AUR62007958' => 'cqu', 'AUR62008481' => 'cqu', 'AUR62021612' => 'cqu', 'BcaB03g12000' => 'bca', 'BcaB03g13119' => 'bca', 'BcaB03g14078' => 'bca', 'BcaB08g34347' => 'bca', 'BcaB08g34348' => 'bca', 'BcaC01g01751' => 'bca', 'BcaC05g26405' => 'bca', 'BcaC05g26406' => 'bca', 'BcaC06g35135' => 'bca', 'BcaC07g38711' => 'bca', 'BcaC07g41613' => 'bca', 'BolC3t19525H' => 'bol', 'BolC5t31176H' => 'bol', 'BolC6t39375H' => 'bol', 'BolC7t42466H' => 'bol', 'BolC8t49265H' => 'bol', 'BolC8t52166H' => 'bol', 'BraA07t29073Z' => 'bra', 'BraA07t31154Z' => 'bra', 'BraA08t34684Z' => 'bra', 'BraA08t35140Z' => 'bra', 'BraA09t41623Z' => 'bra', 'C03p72300' => 'bna', 'C05p24430' => 'bna', 'C06p40560' => 'bna', 'C07p19470' => 'bna', 'C08p16410' => 'bna', 'C08p46160' => 'bna', 'CAN.G1340.15' => 'can', 'CAN.G206.191' => 'can', 'CAN.G442.8' => 'can', 'CAN.G479.42' => 'can', 'CAN.G587.18' => 'can', 'CANSAT50G0006' => 'cansat', 'CANSAT64G3017' => 'cansat', 'CARHR014310' => 'chi', 'CARHR025350' => 'chi', 'CARHR062240' => 'chi', 'Carub.0001s1364' => 'cru', 'Carub.0001s2441' => 'cru', 'Carub.0002s1596' => 'cru', 'Ca_04904_v3' => 'car', 'Ca_21795_v3' => 'car', 'Ca_25949_v3' => 'car', 'Cc04_g13290' => 'ccan', 'Cc07_g03790' => 'ccan', 'Cc11_g12410' => 'ccan', 'CDE04G1089' => 'cde', 'CDE04G1433' => 'cde', 'CDE06G2063' => 'cde', 'CDE07G1318' => 'cde', 'Cfa007616' => 'cfa', 'Cfa008911' => 'cfa', 'Cfa019289' => 'cfa', 'Ciclev10010932m.g' => 'ccl', 'Ciclev10018667m.g' => 'ccl', 'Ciclev10030574m.g' => 'ccl', 'CiPaw.03G092200' => 'cil', 'CiPaw.04G059000' => 'cil', 'CiPaw.05G128200' => 'cil', 'CiPaw.06G089900' => 'cil', 'ClCG04G012020' => 'cla', 'ClCG05G023880' => 'cla', 'ClCG08G010250' => 'cla', 'COL.COLO4_06392' => 'col', 'COL.COLO4_06859' => 'col', 'COL.COLO4_12250' => 'col', 'COL.COLO4_12251' => 'col', 'COL.COLO4_27938' => 'col', 'COL.COLO4_36447' => 'col', 'COL.COLO4_38302' => 'col', 'Cpa.g.c38931' => 'cpa', 'Cpa.g.sc1.82' => 'cpa', 'Cpa.g.sc1.83' => 'cpa', 'Cpa.g.sc13.308' => 'cpa', 'CsaV3_1G005760' => 'csa', 'CsaV3_5G033140' => 'csa', 'CsaV3_6G032450' => 'csa', 'CSS0003937' => 'camsi', 'CSS0006220' => 'camsi', 'CSS0012767' => 'camsi', 'CSS0031318' => 'camsi', 'CSS0031748' => 'camsi', 'CSS0037922' => 'camsi', 'CSS0049375' => 'camsi', 'DCAR_007180' => 'dca', 'DCAR_025403' => 'dca', 'DCAR_026026' => 'dca', 'DCAR_026027' => 'dca', 'DCAR_030980' => 'dca', 'Dinv10677' => 'din', 'Dinv11493' => 'din', 'Dinv16701' => 'din', 'Dinv16702' => 'din', 'Dinv16703' => 'din', 'Dinv33801' => 'din', 'Dinv34112' => 'din', 'Dinv38761' => 'din', 'Dinv38762' => 'din', 'Dinv38763' => 'din', 'Duzib068G0802' => 'dzi', 'Duzib147G0949' => 'dzi', 'Duzib205G0516' => 'dzi', 'Duzib248G0148' => 'dzi', 'Duzib251G0780' => 'dzi', 'Duzib264G1081' => 'dzi', 'Duzib268G0567' => 'dzi', 'ECA232G1758' => 'eca', 'ECA233G2264' => 'eca', 'ECA246G1273' => 'eca', 'EL10Ac5g11082' => 'bvu', 'EL10Ac5g12678' => 'bvu', 'EL10Ac6g14955' => 'bvu', 'Eucgr.B03182' => 'egr', 'Eucgr.G02465' => 'egr', 'FAN02G2125' => 'fan', 'FAN05G3557' => 'fan', 'FAN07G0538' => 'fan', 'FAN08G1032' => 'fan', 'FAN09G4103' => 'fan', 'FAN12G2957' => 'fan', 'FAN13G1067' => 'fan', 'FAN14G2256' => 'fan', 'FAN14G2903' => 'fan', 'FAN14G4724' => 'fan', 'FAN14G5065' => 'fan', 'FAN17G0931' => 'fan', 'FAN18G0277' => 'fan', 'FAN22G0581' => 'fan', 'FvH4_4g30520' => 'fve', 'FvH4_5g14380' => 'fve', 'FvH4_6g47740' => 'fve', 'Glyma.01G054800' => 'gma', 'Glyma.02G113300' => 'gma', 'Glyma.04G165100' => 'gma', 'Glyma.06G198000' => 'gma', 'Glyma.07G227100' => 'gma', 'Glyma.20G027500' => 'gma', 'Gohir.A03G068500' => 'ghi', 'Gohir.A05G305900' => 'ghi', 'Gohir.A12G162600' => 'ghi', 'Gohir.A13G079800' => 'ghi', 'Gohir.D03G095100' => 'ghi', 'Gohir.D05G305900' => 'ghi', 'Gohir.D12G165600' => 'ghi', 'Gohir.D13G079500' => 'ghi', 'Gorai.003G099300' => 'gra', 'Gorai.008G178300' => 'gra', 'Gorai.009G325900' => 'gra', 'Gorai.013G090900' => 'gra', 'GSVIVG01007938001' => 'vvi', 'GSVIVG01011481001' => 'vvi', 'GSVIVG01012173001' => 'vvi', 'HanXRQChr07g0199511' => 'han', 'HanXRQChr08g0211011' => 'han', 'HanXRQChr09g0264111' => 'han', 'HanXRQChr12g0362751' => 'han', 'HanXRQChr14g0448641' => 'han', 'HanXRQChr15g0477041' => 'han', 'HanXRQChr17g0545441' => 'han', 'Haze_07670' => 'cav', 'Haze_11937' => 'cav', 'Haze_14477' => 'cav', 'Hma1.2p1_0060F.1_g033420' => 'hma', 'Hma1.2p1_0354F.1_g133660' => 'hma', 'Hma1.2p1_0357F.1_g134390' => 'hma', 'Hma1.2p1_2073F.1_g313230' => 'hma', 'HPP92_001620' => 'vpl', 'HPP92_017528' => 'vpl', 'Hund02615' => 'sun', 'Hund05858' => 'sun', 'Hund09843' => 'sun', 'Hund25198' => 'sun', 'Lalb_Chr05g0220121' => 'lal', 'Lalb_Chr07g0178221' => 'lal', 'Lalb_Chr09g0329111' => 'lal', 'Lalb_Chr10g0098571' => 'lal', 'Lalb_Chr13g0303011' => 'lal', 'Lalb_Chr17g0340961' => 'lal', 'Lj2g0017216' => 'lja', 'Lj3C1032T12' => 'lonja', 'Lj4g0002221' => 'lja', 'Lj4g0023409' => 'lja', 'Lj6A782T115' => 'lonja', 'Lsat_1_v5_gn_2_88081' => 'lsa', 'Lsat_1_v5_gn_3_56361' => 'lsa', 'Lsat_1_v5_gn_4_170160' => 'lsa', 'Lsat_1_v5_gn_8_48060' => 'lsa', 'Manes.01G030700' => 'mes', 'Manes.05G107500' => 'mes', 'Manes.06G088300' => 'mes', 'Manes.14G082800' => 'mes', 'Mapoly0124s0050' => 'mpo', 'MBI19_g16681_MAGBIO' => 'mbi', 'MD06G1199000' => 'mdo', 'MD09G1059300' => 'mdo', 'MD13G1066200' => 'mdo', 'MD14G1206400' => 'mdo', 'MD16G1065200' => 'mdo', 'MD17G1054900' => 'mdo', 'MD17G1055200' => 'mdo', 'Medtr4g082510' => 'mtr', 'Medtr4g109190' => 'mtr', 'Medtr5g043430' => 'mtr', 'MELO3C002006.2' => 'cme', 'MELO3C011433.2' => 'cme', 'MELO3C012134.2' => 'cme', 'Migut.E00063' => 'egut', 'Migut.H00664' => 'egut', 'Migut.L01226' => 'egut', 'MSTRG.13440' => 'ama', 'MSTRG.2324' => 'ama', 'MSTRG.23907' => 'ama', 'MSTRG.4447' => 'ama', 'MSTRG.727' => 'ama', 'MSTRG.7767' => 'ama', 'MSTRG.9614' => 'ama', 'Nitab4.5_0000014g0250' => 'nta', 'Nitab4.5_0000334g0200' => 'nta', 'Nitab4.5_0000520g0040' => 'nta', 'Nitab4.5_0000565g0020' => 'nta', 'Nitab4.5_0000720g0030' => 'nta', 'Nitab4.5_0001211g0060' => 'nta', 'Nitab4.5_0002756g0060' => 'nta', 'Nitab4.5_0002832g0020' => 'nta', 'Nitab4.5_0003021g0030' => 'nta', 'Nitab4.5_0006673g0020' => 'nta', 'Nitab4.5_0008573g0010' => 'nta', 'Nn1g09175' => 'nnu', 'Nn3g17370' => 'nnu', 'Nn4g23320' => 'nnu', 'Nn5g27508' => 'nnu', 'Nn8g40395' => 'nnu', 'Oeu003341.1' => 'oeu', 'Oeu010233.1' => 'oeu', 'Oeu016231.1' => 'oeu', 'Oeu016756.1' => 'oeu', 'Oeu021094.1' => 'oeu', 'Oeu028260.1' => 'oeu', 'Oeu047264.1' => 'oeu', 'Oeu055092.1' => 'oeu', 'Oeu057649.1' => 'oeu', 'Os03g0758600' => 'osa', 'Os12g0577800' => 'osa', 'Peaxi162Scf00013g00051' => 'pax', 'Peaxi162Scf00097g00712' => 'pax', 'Peaxi162Scf00166g00945' => 'pax', 'Peaxi162Scf00274g00008' => 'pax', 'Peaxi162Scf00364g00128' => 'pax', 'PGR004G1789' => 'pgr', 'PGR102G1162' => 'pgr', 'PGR119G0403' => 'pgr', 'PGSC0003DMG400002849' => 'stu', 'PGSC0003DMG400024659' => 'stu', 'PGSC0003DMG400033051' => 'stu', 'PGSC0003DMG401001346' => 'stu', 'PGSC0003DMG401028385' => 'stu', 'PGSC0003DMG402001346' => 'stu', 'PGSC0003DMG402028385' => 'stu', 'Phvul.002G069600' => 'pvu', 'Phvul.002G167700' => 'pvu', 'Phvul.009G184400' => 'pvu', 'Potri.004G125900' => 'ptr', 'Potri.008G092800' => 'ptr', 'Potri.010G162000' => 'ptr', 'Potri.017G088900' => 'ptr', 'Prupe.1G281700' => 'ppe', 'Prupe.3G261200' => 'ppe', 'Prupe.5G199800' => 'ppe', 'Psat2g120520' => 'psa', 'Psat2g128440' => 'psa', 'Psat4g048920' => 'psa', 'Psat5g041560' => 'psa', 'Psat7g134840' => 'psa', 'PSO017G1876' => 'pso', 'PSO017G3159' => 'pso', 'PSO478G3214' => 'pso', 'PSO478G3501' => 'pso', 'QL03p070806' => 'qlo', 'QL10p018539' => 'qlo', 'RcHm_v2.0_Chr2g0166861' => 'rch', 'RcHm_v2.0_Chr4g0438891' => 'rch', 'RcHm_v2.0_Chr7g0182271' => 'rch', 'RcHm_v2.0_Chr7g0182291' => 'rch', 'Rhsim08G0149900' => 'rsi', 'Rhsim10G0034500' => 'rsi', 'Rhsim12G0077000' => 'rsi', 'Rhsim12G0134000' => 'rsi', 'Sabra04G0066600' => 'sbr', 'Sabra08G0069600' => 'sbr', 'Sabra10G0123100' => 'sbr', 'Sabra17G0078600' => 'sbr', 'SalBow2G1415' => 'sbo', 'SalBow7G0805' => 'sbo', 'SalBow8G2082' => 'sbo', 'Sc04g0002960' => 'sci', 'Sc04g0007760' => 'sci', 'Sc11g0002250' => 'sci', 'Sed0011907' => 'sed', 'Sed0017185' => 'sed', 'Sed0018687' => 'sed', 'Sed0025408' => 'sed', 'SEGI_03234' => 'sgi', 'SEGI_07957' => 'sgi', 'SEGI_10296' => 'sgi', 'SEGI_16187' => 'sgi', 'SEGI_22180' => 'sgi', 'SGA_v2.0_scaffold287G47150' => 'sas', 'SGA_v2.0_scaffold36G14432' => 'sas', 'SGA_v2.0_scaffold413G51167' => 'sas', 'SGA_v2.0_scaffold63G21635' => 'sas', 'SHI27316' => 'shi', 'SMO358G0165' => 'smo', 'Solyc02g088480.3' => 'sly', 'Solyc03g115590.4' => 'sly', 'Solyc04g005500.3' => 'sly', 'Solyc05g012640.3' => 'sly', 'Solyc05g012650.4' => 'sly', 'Solyc06g069630.4' => 'sly', 'Sopen02g033190' => 'spe', 'Sopen03g034580' => 'spe', 'Sopen04g001520' => 'spe', 'Sopen05g007470' => 'spe', 'Sopen05g007480' => 'spe', 'Sopen06g026930' => 'spe', 'Sp1g12010' => 'spa', 'Sp1g22180' => 'spa', 'TAR371G0889' => 'tar', 'TAR371G1209' => 'tar', 'TAR374G1508' => 'tar', 'TAR622G0794' => 'tar', 'TAR629G1896' => 'tar', 'THA.LOC104801814' => 'tha', 'THA.LOC104808598' => 'tha', 'THA.LOC104822024' => 'tha', 'THA.LOC104822901' => 'tha', 'Thecc.02G336800' => 'tca', 'Thecc.03G095800' => 'tca', 'Thecc.04G089400' => 'tca', 'Thecc.07G038300' => 'tca', 'Thhalv10006678m.g' => 'esa', 'Thhalv10006734m.g' => 'esa', 'Thhalv10018101m.g' => 'esa', 'TPR.G1992' => 'tpr', 'TPR.G22408' => 'tpr', 'TPR.G34059' => 'tpr', 'TWI31G0752' => 'twi', 'TWI32G0259' => 'twi', 'TWI60G0848' => 'twi', 'TWI75G0091' => 'twi', 'TWI79G1594' => 'twi', 'unitig_21.g20860' => 'ugi', 'unitig_22.g5554' => 'ugi', 'unitig_52.g17162' => 'ugi', 'unitig_52.g17163' => 'ugi', 'unitig_52.g17164' => 'ugi', 'unitig_62.g23693' => 'ugi', 'unitig_736.g22242' => 'ugi', 'unitig_899.g15161' => 'ugi', 'vmacro01333' => 'vma', 'vmacro05592' => 'vma', 'vmacro05671' => 'vma', 'vmacro16367' => 'vma', 'vmacro17582' => 'vma', 'VMungo0251G0497' => 'vmu', 'VMungo1215G2164' => 'vmu', 'VMungo1309G1429' => 'vmu', 'Zm00001eb029680' => 'zma', 'Zm00001eb057910' => 'zma', 'Zm00001eb080060' => 'zma', 'Zm00001eb214520' => 'zma', 'Zm00001eb410180' => 'zma' ) $gf_id = 'HOM05D001536' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001536' ) $data_identifier = 'HOM05D001536' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 7, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 2, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 6, 'bra' => (int) 5, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 7, 'cpa' => (int) 4, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 10, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 2, 'fan' => (int) 14, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 7, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 6, 'lja' => (int) 3, 'lonja' => (int) 2, 'lsa' => (int) 4, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 9, 'osa' => (int) 2, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 2, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 8, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410180' $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